- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2934: trackster: fixed browser crashing (were drawin...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/979534de254d changeset: 2934:979534de254d user: Kanwei Li <kanwei(a)gmail.com> date: Thu Oct 29 18:28:11 2009 -0400 description: trackster: fixed browser crashing (were drawing huge canvas tiles because of resolution restriction), implemented simple LRU diffstat: static/scripts/lrucache.js | 238 --------------------------------------- static/scripts/packed/lrucache.js | 1 - static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 46 ++++++- templates/tracks/browser.mako | 2 +- 5 files changed, 39 insertions(+), 250 deletions(-) diffs (359 lines): diff -r 28ec4708840f -r 979534de254d static/scripts/lrucache.js --- a/static/scripts/lrucache.js Thu Oct 29 17:57:30 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,238 +0,0 @@ -/* -MIT LICENSE -Copyright (c) 2007 Monsur Hossain (http://www.monsur.com) - -Permission is hereby granted, free of charge, to any person -obtaining a copy of this software and associated documentation -files (the "Software"), to deal in the Software without -restriction, including without limitation the rights to use, -copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the -Software is furnished to do so, subject to the following -conditions: - -The above copyright notice and this permission notice shall be -included in all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES -OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT -HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, -WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR -OTHER DEALINGS IN THE SOFTWARE. -*/ - -// **************************************************************************** -// CachePriority ENUM -// An easier way to refer to the priority of a cache item -var CachePriority = { - Low: 1, - Normal: 2, - High: 4 -} - -// **************************************************************************** -// Cache constructor -// Creates a new cache object -// INPUT: maxSize (optional) - indicates how many items the cache can hold. -// default is -1, which means no limit on the -// number of items. -function Cache(maxSize) { - this.items = {}; - this.count = 0; - if (maxSize == null) - maxSize = -1; - this.maxSize = maxSize; - this.fillFactor = .75; - this.purgeSize = Math.round(this.maxSize * this.fillFactor); - - this.stats = {} - this.stats.hits = 0; - this.stats.misses = 0; -} - -// **************************************************************************** -// Cache.getItem -// retrieves an item from the cache, returns null if the item doesn't exist -// or it is expired. -// INPUT: key - the key to load from the cache -Cache.prototype.getItem = function(key) { - - // retrieve the item from the cache - var item = this.items[key]; - - if (item != null) { - if (!this._isExpired(item)) { - // if the item is not expired - // update its last accessed date - item.lastAccessed = new Date().getTime(); - } else { - // if the item is expired, remove it from the cache - this._removeItem(key); - item = null; - } - } - - // return the item value (if it exists), or null - var returnVal = null; - if (item != null) { - returnVal = item.value; - this.stats.hits++; - } else { - this.stats.misses++; - } - return returnVal; -} - -// **************************************************************************** -// Cache.setItem -// sets an item in the cache -// parameters: key - the key to refer to the object -// value - the object to cache -// options - an optional parameter described below -// the last parameter accepts an object which controls various caching options: -// expirationAbsolute: the datetime when the item should expire -// expirationSliding: an integer representing the seconds since -// the last cache access after which the item -// should expire -// priority: How important it is to leave this item in the cache. -// You can use the values CachePriority.Low, .Normal, or -// .High, or you can just use an integer. Note that -// placing a priority on an item does not guarantee -// it will remain in cache. It can still be purged if -// an expiration is hit, or if the cache is full. -// callback: A function that gets called when the item is purged -// from cache. The key and value of the removed item -// are passed as parameters to the callback function. -Cache.prototype.setItem = function(key, value, options) { - - function CacheItem(k, v, o) { - if ((k == null) || (k == '')) - throw new Error("key cannot be null or empty"); - this.key = k; - this.value = v; - if (o == null) - o = {}; - if (o.expirationAbsolute != null) - o.expirationAbsolute = o.expirationAbsolute.getTime(); - if (o.priority == null) - o.priority = CachePriority.Normal; - this.options = o; - this.lastAccessed = new Date().getTime(); - } - - // add a new cache item to the cache - if (this.items[key] != null) - this._removeItem(key); - this._addItem(new CacheItem(key, value, options)); - - // if the cache is full, purge it - if ((this.maxSize > 0) && (this.count > this.maxSize)) { - this._purge(); - } -} - -// **************************************************************************** -// Cache.clear -// Remove all items from the cache -Cache.prototype.clear = function() { - - // loop through each item in the cache and remove it - for (var key in this.items) { - this._removeItem(key); - } -} - -// **************************************************************************** -// Cache._purge (PRIVATE FUNCTION) -// remove old elements from the cache -Cache.prototype._purge = function() { - - var tmparray = new Array(); - - // loop through the cache, expire items that should be expired - // otherwise, add the item to an array - for (var key in this.items) { - var item = this.items[key]; - if (this._isExpired(item)) { - this._removeItem(key); - } else { - tmparray.push(item); - } - } - - if (tmparray.length > this.purgeSize) { - - // sort this array based on cache priority and the last accessed date - tmparray = tmparray.sort(function(a, b) { - if (a.options.priority != b.options.priority) { - return b.options.priority - a.options.priority; - } else { - return b.lastAccessed - a.lastAccessed; - } - }); - - // remove items from the end of the array - while (tmparray.length > this.purgeSize) { - var ritem = tmparray.pop(); - this._removeItem(ritem.key); - } - } -} - -// **************************************************************************** -// Cache._addItem (PRIVATE FUNCTION) -// add an item to the cache -Cache.prototype._addItem = function(item) { - this.items[item.key] = item; - this.count++; -} - -// **************************************************************************** -// Cache._removeItem (PRIVATE FUNCTION) -// Remove an item from the cache, call the callback function (if necessary) -Cache.prototype._removeItem = function(key) { - var item = this.items[key]; - delete this.items[key]; - this.count--; - - // if there is a callback function, call it at the end of execution - if (item.options.callback != null) { - var callback = function() { - item.options.callback(item.key, item.value); - } - setTimeout(callback, 0); - } -} - -// **************************************************************************** -// Cache._isExpired (PRIVATE FUNCTION) -// Returns true if the item should be expired based on its expiration options -Cache.prototype._isExpired = function(item) { - var now = new Date().getTime(); - var expired = false; - if ((item.options.expirationAbsolute) && (item.options.expirationAbsolute < now)) { - // if the absolute expiration has passed, expire the item - expired = true; - } - if ((expired == false) && (item.options.expirationSliding)) { - // if the sliding expiration has passed, expire the item - var lastAccess = item.lastAccessed + (item.options.expirationSliding * 1000); - if (lastAccess < now) { - expired = true; - } - } - return expired; -} - -Cache.prototype.toHtmlString = function() { - var returnStr = this.count + " item(s) in cache<br /><ul>"; - for (var key in this.items) { - var item = this.items[key]; - returnStr = returnStr + "<li>" + item.key.toString() + " = " + item.value.toString() + "</li>"; - } - returnStr = returnStr + "</ul>"; - return returnStr; -} diff -r 28ec4708840f -r 979534de254d static/scripts/packed/lrucache.js --- a/static/scripts/packed/lrucache.js Thu Oct 29 17:57:30 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -var CachePriority={Low:1,Normal:2,High:4};function Cache(a){this.items={};this.count=0;if(a==null){a=-1}this.maxSize=a;this.fillFactor=0.75;this.purgeSize=Math.round(this.maxSize*this.fillFactor);this.stats={};this.stats.hits=0;this.stats.misses=0}Cache.prototype.getItem=function(a){var c=this.items[a];if(c!=null){if(!this._isExpired(c)){c.lastAccessed=new Date().getTime()}else{this._removeItem(a);c=null}}var b=null;if(c!=null){b=c.value;this.stats.hits++}else{this.stats.misses++}return b};Cache.prototype.setItem=function(c,d,b){function a(f,e,g){if((f==null)||(f=="")){throw new Error("key cannot be null or empty")}this.key=f;this.value=e;if(g==null){g={}}if(g.expirationAbsolute!=null){g.expirationAbsolute=g.expirationAbsolute.getTime()}if(g.priority==null){g.priority=CachePriority.Normal}this.options=g;this.lastAccessed=new Date().getTime()}if(this.items[c]!=null){this._removeItem(c)}this._addItem(new a(c,d,b));if((this.maxSize>0)&&(this.count>this.maxSize)){this._purge()}} ;Cache.prototype.clear=function(){for(var a in this.items){this._removeItem(a)}};Cache.prototype._purge=function(){var d=new Array();for(var a in this.items){var b=this.items[a];if(this._isExpired(b)){this._removeItem(a)}else{d.push(b)}}if(d.length>this.purgeSize){d=d.sort(function(f,e){if(f.options.priority!=e.options.priority){return e.options.priority-f.options.priority}else{return e.lastAccessed-f.lastAccessed}});while(d.length>this.purgeSize){var c=d.pop();this._removeItem(c.key)}}};Cache.prototype._addItem=function(a){this.items[a.key]=a;this.count++};Cache.prototype._removeItem=function(a){var b=this.items[a];delete this.items[a];this.count--;if(b.options.callback!=null){var c=function(){b.options.callback(b.key,b.value)};setTimeout(c,0)}};Cache.prototype._isExpired=function(c){var a=new Date().getTime();var b=false;if((c.options.expirationAbsolute)&&(c.options.expirationAbsolute<a)){b=true}if((b==false)&&(c.options.expirationSliding)){var d=c.lastAccessed+(c.options. expirationSliding*1000);if(d<a){b=true}}return b};Cache.prototype.toHtmlString=function(){var b=this.count+" item(s) in cache<br /><ul>";for(var a in this.items){var c=this.items[a];b=b+"<li>"+c.key.toString()+" = "+c.value.toString()+"</li>"}b=b+"</ul>";return b}; \ No newline at end of file diff -r 28ec4708840f -r 979534de254d static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Thu Oct 29 17:57:30 2009 -0400 +++ b/static/scripts/packed/trackster.js Thu Oct 29 18:28:11 2009 -0400 @@ -1,1 +1,1 @@ -var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",CACHED_TILES=50,CACHED_DATA=20;function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).sh ow();$("#low").text(commatize(this.low));$("#high").text(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<5){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TI LES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,c=this.view.high,e=c-i;var b=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));b=Math.max(b,1);b=Math.min(b,100000);var l=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(l);var j=this.content_div.width(),d=this.content_div.height(),m=j/e;var g;var a=Math.floor(i/b/DENSITY);while((a*DENSITY*b)<c){var k=this.view.zoom_level+"_"+a;if(this.tile_cache[k]){g=this.tile_cache[k];var f=a*DENSITY*b;g.css({left:(f-this.view.low)*m});l.append(g)}else{g=this.draw_tile(b,a,l,m,d)}if(g){this.tile_cache[k]=g}a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style= 'position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(b){if(!b||b=="error"){a.content_div.addClass("error").text(DATA_ERROR)}else{if(b=="no data"){a.content_div.addClass("nodata").text(DATA_NONE)}else{a.content_div.css("height",a.height_px+"px");a.min_value=b.min;a.max_value=b.max;a.vertical_range=a.max_value-a.min_value;a.view.redraw()}}})},get_data:f unction(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[e]=g;$(document).trigger("redraw")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);th is.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.content_div.addClass("error").text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.content_div.addClass("nodata").text(DATA_NONE)}else{a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}})},calc_slots:function(o){var c=[],b=this.container_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k=Math.floor(Math.max(e,(n.start-e)*g));k-=m.mea sureText(n.name).width;l=Math.ceil(Math.min(a,(n.end-e)*g))}else{k=Math.floor(Math.max(e,(n.start-e)*b));l=Math.ceil(Math.min(a,(n.end-e)*b))}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(t,y,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var z=y*DENSITY*t,b=(y+1)*DENSITY*t,o=DENSITY*t;var r=Math.ceil(o*n),q=this.height_px,p=$("<canvas class='tile'></canvas>");p.css({position:"absolute",top:0,left:(z-this.view.low)*n});p.get(0).width=r;p.get(0).height=q;var s=p.get(0).getContext("2d");s.fillStyle="#000";s.font="10px monospace";s.textAlign="right";var v=0;for(var w=0,x=this.values.length;w<x;w++){var f=this.values[w];if(f.start<=b&&f.end>=z){var e=Math.floor(Math.max(0,(f.start-z)*n)),h=Math.ceil(Math.min(r,(f.end-z)*n)),d=this.slots[f.name]*this.vertical_gap;s.fillRect(e,d+5,h-e,1);if(this.showing_labels&&s.fillText){s.fillText(f.name,e,d+8)}var c,D;if(f.exon_start&&f.exon_end){c=Math.floor(Math.max(0,(f.exon_start-z)*n));D=Math.ceil(Math.min(r,(f.exon_end-z)*n));s.fillRect(c,d+4,D-c,3)}if(f.blocks){for(var u=0,B=f.blocks.length;u<B;u++){var m=f.blocks[u],l=Math.floor(Math.max(0,(m[0]-z)*n)),A=Math.ceil(Math.min(r,(m[1]-z)*n));var a=3,C=4;if(c&&l>=c&&A<=D){a=5;C=3}s.fillRect(l,d+C,A-l,a)}}v++}}g.append(p);return p}}); \ No newline at end of file +var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES=5,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(l eft_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e =this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){thi s.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TILES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var h=this.view.low,d=this.view.high,e=d-h;var c=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));c=Math.max(c,0.1);c=Math.min(c,1000000);var j=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(j);var k=this.content_div.width()/e;var g;var a=Math.floor(h/c/DENSITY);while((a*DENSITY*c)<d){var i=this.view.zoom_level+"_"+a;var b=this.tile_cache.get(i);if(b){var f=a*DENSITY*c;b.css({left:(f-this.view.low)*k});j.append(b)}else{g=this.draw_tile(c,a,j,k)}if(g){this.tile_cache.set(i,g)}a+=1}}});var LabelTrack=function(a){Track.ca ll(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dat aset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px",});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[e]=g;$(document).trigger("redra w")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(FeatureTrack.prototype,TiledTrack.pro totype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},calc_slots:function(o){var c=[],b=this.container_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k=Math.floor(Math.max(e,(n.star t-e)*g));k-=m.measureText(n.name).width;l=Math.ceil(Math.min(a,(n.end-e)*g))}else{k=Math.floor(Math.max(e,(n.start-e)*b));l=Math.ceil(Math.min(a,(n.end-e)*b))}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(w,B,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var C=B*DENSITY*w,c=(B+1)*DENSITY*w,q=DENSITY*w;var u=Math.ceil(q*n),t=this.height_px,s=$("<canvas class='tile'></canvas>");s.css({position:"absolute",top:0,left:(C-this.view.low)*n});s.get(0).width=u;s.get(0).height=t;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font="10px monospac e";v.textAlign="right";var y=0;for(var z=0,A=this.values.length;z<A;z++){var f=this.values[z];if(f.start<=c&&f.end>=C){var e=Math.floor(Math.max(0,(f.start-C)*n)),h=Math.ceil(Math.min(u,(f.end-C)*n)),d=this.slots[f.name]*this.vertical_gap;var a,G,b=null,o=null;if(f.thick_start&&f.thick_end){b=Math.floor(Math.max(0,(f.thick_start-C)*n));o=Math.ceil(Math.min(u,(f.thick_end-C)*n))}if(!this.showing_labels){v.fillRect(e,d+5,h-e,1)}else{if(v.fillText){v.fillText(f.name,e-1,d+8)}var E=f.blocks;if(E){if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND}else{if(f.strand=="-"){v.fillStyle=LEFT_STRAND}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}for(var x=0,F=E.length;x<F;x++){var m=E[x],l=Math.floor(Math.max(0,(m[0]-C)*n)),D=Math.ceil(Math.min(u,(m[1]-C)*n));a=5;G=3;v.fillRect(l,d+G,D-l,a);if(b&&(l<o||D>b)){a=9;G=1;var r=Math.max(l,b),p=Math.min(D,o);v.fillRect(r,d+G,p-r,a)}}}else{a=9;G=1;v.fillRect(e,d+G,h-e,a);if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND_INV}els e{if(f.strand=="-"){v.fillStyle=LEFT_STRAND_INV}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}}}y++}}g.append(s);return s}}); \ No newline at end of file diff -r 28ec4708840f -r 979534de254d static/scripts/trackster.js --- a/static/scripts/trackster.js Thu Oct 29 17:57:30 2009 -0400 +++ b/static/scripts/trackster.js Thu Oct 29 18:28:11 2009 -0400 @@ -7,7 +7,7 @@ DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", DATA_LOADING = "Loading data...", - CACHED_TILES = 50, + CACHED_TILES = 5, CACHED_DATA = 20, CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"), RIGHT_STRAND, LEFT_STRAND; @@ -42,6 +42,36 @@ } return number; } + +var Cache = function( num_elements ) { + this.num_elements = num_elements; + this.obj_cache = {}; + this.key_ary = []; +} +$.extend( Cache.prototype, { + get: function( key ) { + var index = this.key_ary.indexOf(key); + if (index != -1) { + // Move to the end + this.key_ary.splice(index, 1); + this.key_ary.push(key); + } + return this.obj_cache[key]; + }, + set: function( key, value ) { + if (!this.obj_cache[key]) { + if (this.key_ary.length >= this.num_elements) { + // Remove first element + var deleted_key = this.key_ary.shift(); + delete this.obj_cache[deleted_key]; + } + this.key_ary.push(key); + } + this.obj_cache[key] = value; + return value; + } +}); + var View = function( chrom, max_high ) { this.chrom = chrom; this.tracks = []; @@ -138,16 +168,14 @@ range = high - low; var resolution = Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) ); - resolution = Math.max( resolution, 1 ); - resolution = Math.min( resolution, 100000 ); + resolution = Math.max( resolution, 0.1 ); + resolution = Math.min( resolution, 1000000 ); var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); this.content_div.append( parent_element ); - var w = this.content_div.width(), - h = this.content_div.height(), - w_scale = w / range; + var w_scale = this.content_div.width() / range; var tile_element; // Index of first tile that overlaps visible region @@ -155,7 +183,7 @@ while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache var key = this.view.zoom_level + "_" + tile_index; - var cached = this.tile_cache.getItem(key); + var cached = this.tile_cache.get(key); if ( cached ) { // console.log("cached tile"); var tile_low = tile_index * DENSITY * resolution; @@ -165,10 +193,10 @@ // Our responsibility to move the element to the new parent parent_element.append( cached ); } else { - tile_element = this.draw_tile( resolution, tile_index, parent_element, w_scale, h ); + tile_element = this.draw_tile( resolution, tile_index, parent_element, w_scale ); } if ( tile_element ) { - this.tile_cache.setItem(key, tile_element); + this.tile_cache.set(key, tile_element); } tile_index += 1; } diff -r 28ec4708840f -r 979534de254d templates/tracks/browser.mako --- a/templates/tracks/browser.mako Thu Oct 29 17:57:30 2009 -0400 +++ b/templates/tracks/browser.mako Thu Oct 29 18:28:11 2009 -0400 @@ -7,7 +7,7 @@ <%def name="javascripts()"> ${parent.javascripts()} -${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "lrucache", "trackster" )} +${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster" )} <script type="text/javascript">

1 0

[hg] galaxy 2933: updated rgenetics test files
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/28ec4708840f changeset: 2933:28ec4708840f user: Ross Lazarus <ross.lazarus(a)gmail.com> date: Thu Oct 29 17:57:30 2009 -0400 description: updated rgenetics test files diffstat: test-data/tinywga.bed | 2 +- test-data/tinywga.bim | 35 ++++++++--- test-data/tinywga.fam | 130 +++++++++++++------------------------------ test-data/tinywga.map | 35 ++++++++--- test-data/tinywga.ped | 130 +++++++++++++------------------------------ test-data/tinywga.pphe | 42 ++++++++++++++ 6 files changed, 173 insertions(+), 201 deletions(-) diffs (400 lines): diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.bed --- a/test-data/tinywga.bed Thu Oct 29 13:34:44 2009 -0400 +++ b/test-data/tinywga.bed Thu Oct 29 17:57:30 2009 -0400 @@ -1,1 +1,1 @@ -lÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿï¾î¸ÿÿüþ¿ÿ¿ûú¿¿ï/ÿÿþÿï¯ê¸ëê°®¾î®ãê¸;ì/âïú¯ï¯Îê¼ïâ°¯þÏªã¯ø+ì?âÿú¯ïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïÿÿÿÿÿºÿÿþ¯þï¿ÿ»ÿÿþÿÿÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿÿÿÿÿþïÿÿÿþÿÿÿÿûÿûÿÿÿ»ÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïëÿê¾ÿºúïþ¯îë¿þ;¯>âïþ» \ No newline at end of file +lÿëþ¿¾+êóª¿ü £ïªîþ¨êÿïªûÿÿÿÿÿÿþï®¨ª"ëú £ïªîþ¨ÿÿ»ÿÿïïþÿèÿþ"ÿ«ïªîþ¨:*ÿïêüº.«ë:*ÿïêüº.«ëÿÿÿÿ¯ÿ¿ïþ¿ÿþªÿ¯û¿ïþ¿:*»ïêìª,«À:*»ïêìª,«Àÿëþ¿¾+êóª¿ÿÿÿÿûÿúÿÿÿÿÿÿÿÿÿ¿þ¿ÿëþ¿¾+êóª¿ºûÿÿ¿»ÿÿþ¿êÿÿªûÿÿÿÿÿºûÿÿ¿»ÿÿþ¿mÿÿÿýÿÿÿÿÿ ú¢ª±«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü( \ No newline at end of file diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.bim --- a/test-data/tinywga.bim Thu Oct 29 13:34:44 2009 -0400 +++ b/test-data/tinywga.bim Thu Oct 29 17:57:30 2009 -0400 @@ -1,10 +1,25 @@ -22 rs5992809 16.5965 16596539 0 C -22 rs12168131 16.6573 16657262 G A -22 rs390041 16.6629 16662916 T C -22 rs437633 16.6697 16669684 A G -22 rs450960 16.6909 16690858 T C -22 rs450975 16.6909 16690887 T C -22 rs451740 16.6912 16691174 T C -22 rs8139723 16.6917 16691696 T C -22 rs405490 16.6922 16692175 G A -22 rs415170 16.6935 16693517 G C +22 rs2283802 0 21784722 4 2 +22 rs2267000 0 21785366 4 2 +22 rs16997606 0 21794754 1 3 +22 rs4820537 0 21794810 1 3 +22 rs3788347 0 21797804 3 1 +22 rs756632 0 21799918 4 2 +22 rs4820539 0 21807970 1 3 +22 rs2283804 0 21820335 1 2 +22 rs2267006 0 21820990 3 1 +22 rs4822363 0 21821000 4 2 +22 rs5751592 0 21827674 4 2 +22 rs5759608 0 21832708 2 4 +22 rs5759612 0 21833170 3 1 +22 rs2267009 0 21860168 3 4 +22 rs2267010 0 21864366 3 1 +22 rs5759636 0 21868698 4 2 +22 rs2071436 0 21871488 4 2 +22 rs2267013 0 21875879 3 1 +22 rs6003566 0 21889806 3 1 +22 rs2256725 0 21892891 2 1 +22 rs12160770 0 21892925 1 3 +22 rs5751611 0 21896019 2 4 +22 rs762601 0 21898858 1 3 +22 rs2156921 0 21899063 3 1 +22 rs4822375 0 21905642 1 3 diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.fam --- a/test-data/tinywga.fam Thu Oct 29 13:34:44 2009 -0400 +++ b/test-data/tinywga.fam Thu Oct 29 17:57:30 2009 -0400 @@ -1,90 +1,40 @@ -CH18526 NA18526 0 0 2 1 -CH18524 NA18524 0 0 1 1 -CH18529 NA18529 0 0 2 1 -CH18558 NA18558 0 0 1 1 -CH18532 NA18532 0 0 2 1 -CH18561 NA18561 0 0 1 1 -CH18562 NA18562 0 0 1 1 -CH18537 NA18537 0 0 2 2 -CH18603 NA18603 0 0 1 2 -CH18540 NA18540 0 0 2 1 -CH18605 NA18605 0 0 1 1 -CH18542 NA18542 0 0 2 1 -CH18545 NA18545 0 0 2 1 -CH18572 NA18572 0 0 1 2 -CH18547 NA18547 0 0 2 2 -CH18609 NA18609 0 0 1 1 -CH18550 NA18550 0 0 2 1 -CH18608 NA18608 0 0 1 1 -CH18552 NA18552 0 0 2 1 -CH18611 NA18611 0 0 1 1 -CH18555 NA18555 0 0 2 1 -CH18564 NA18564 0 0 2 2 -CH18566 NA18566 0 0 2 1 -CH18563 NA18563 0 0 1 1 -CH18570 NA18570 0 0 2 1 -CH18612 NA18612 0 0 1 2 -CH18571 NA18571 0 0 2 1 -CH18620 NA18620 0 0 1 1 -CH18621 NA18621 0 0 1 1 -CH18594 NA18594 0 0 2 1 -CH18622 NA18622 0 0 1 2 -CH18573 NA18573 0 0 2 2 -CH18623 NA18623 0 0 1 1 -CH18576 NA18576 0 0 2 1 -CH18577 NA18577 0 0 2 1 -CH18624 NA18624 0 0 1 1 -CH18579 NA18579 0 0 2 1 -CH18632 NA18632 0 0 1 2 -CH18582 NA18582 0 0 2 1 -CH18633 NA18633 0 0 1 1 -CH18635 NA18635 0 0 1 2 -CH18592 NA18592 0 0 2 1 -CH18636 NA18636 0 0 1 1 -CH18593 NA18593 0 0 2 2 -CH18637 NA18637 0 0 1 1 -JA18942 NA18942 0 0 2 2 -JA18940 NA18940 0 0 1 2 -JA18951 NA18951 0 0 2 2 -JA18943 NA18943 0 0 1 2 -JA18947 NA18947 0 0 2 2 -JA18944 NA18944 0 0 1 2 -JA18945 NA18945 0 0 1 2 -JA18949 NA18949 0 0 2 2 -JA18948 NA18948 0 0 1 2 -JA18952 NA18952 0 0 1 2 -JA18956 NA18956 0 0 2 2 -JA18964 NA18964 0 0 2 2 -JA18953 NA18953 0 0 1 1 -JA18968 NA18968 0 0 2 2 -JA18959 NA18959 0 0 1 2 -JA18969 NA18969 0 0 2 1 -JA18960 NA18960 0 0 1 2 -JA18961 NA18961 0 0 1 2 -JA18972 NA18972 0 0 2 2 -JA18965 NA18965 0 0 1 2 -JA18973 NA18973 0 0 2 2 -JA18966 NA18966 0 0 1 2 -JA18975 NA18975 0 0 2 2 -JA18967 NA18967 0 0 1 2 -JA18976 NA18976 0 0 2 1 -JA18978 NA18978 0 0 2 2 -JA18970 NA18970 0 0 1 1 -JA18980 NA18980 0 0 2 2 -JA18995 NA18995 0 0 1 1 -JA18981 NA18981 0 0 2 2 -JA18971 NA18971 0 0 1 2 -JA18974 NA18974 0 0 1 1 -JA18987 NA18987 0 0 2 2 -JA18990 NA18990 0 0 1 1 -JA18991 NA18991 0 0 2 2 -JA18994 NA18994 0 0 1 2 -JA18992 NA18992 0 0 2 2 -JA18997 NA18997 0 0 2 2 -JA18998 NA18998 0 0 2 2 -JA19000 NA19000 0 0 1 2 -JA19005 NA19005 0 0 1 2 -JA18999 NA18999 0 0 2 2 -JA19007 NA19007 0 0 1 2 -JA19003 NA19003 0 0 2 2 -JA19012 NA19012 0 0 1 2 +101 1 3 2 2 2 +101 2 0 0 2 1 +101 3 0 0 1 1 +105 1 3 2 2 2 +105 2 0 0 2 1 +105 3 0 0 1 1 +112 1 3 2 1 2 +112 2 0 0 2 1 +112 3 0 0 1 1 +117 1 3 2 2 2 +117 2 0 0 2 1 +117 3 0 0 1 1 +12 1 3 2 1 2 +12 2 0 0 2 1 +12 3 0 0 1 1 +13 1 3 2 1 2 +13 2 0 0 2 1 +13 3 0 0 1 1 +1334 1 10 11 1 2 +1334 10 0 0 1 1 +1334 11 0 0 2 1 +1334 12 0 0 1 1 +1334 13 0 0 2 1 +1334 2 12 13 2 2 +1340 1 9 10 1 2 +1340 10 0 0 2 1 +1340 11 0 0 1 1 +1340 12 0 0 2 1 +1340 2 11 12 2 2 +1340 9 0 0 1 1 +1341 1 11 12 1 1 +1341 11 0 0 1 1 +1341 12 0 0 2 1 +1341 13 0 0 1 1 +1341 14 0 0 2 1 +1341 2 13 14 2 1 +1344 1 12 13 1 1 +1344 12 0 0 1 1 +1344 13 0 0 2 1 +1345 12 0 0 1 1 diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.map --- a/test-data/tinywga.map Thu Oct 29 13:34:44 2009 -0400 +++ b/test-data/tinywga.map Thu Oct 29 17:57:30 2009 -0400 @@ -1,10 +1,25 @@ -22 rs5992809 16.5965 16596539 -22 rs12168131 16.6573 16657262 -22 rs390041 16.6629 16662916 -22 rs437633 16.6697 16669684 -22 rs450960 16.6909 16690858 -22 rs450975 16.6909 16690887 -22 rs451740 16.6912 16691174 -22 rs8139723 16.6917 16691696 -22 rs405490 16.6922 16692175 -22 rs415170 16.6935 16693517 +22 rs2283802 0 21784722 +22 rs2267000 0 21785366 +22 rs16997606 0 21794754 +22 rs4820537 0 21794810 +22 rs3788347 0 21797804 +22 rs756632 0 21799918 +22 rs4820539 0 21807970 +22 rs2283804 0 21820335 +22 rs2267006 0 21820990 +22 rs4822363 0 21821000 +22 rs5751592 0 21827674 +22 rs5759608 0 21832708 +22 rs5759612 0 21833170 +22 rs2267009 0 21860168 +22 rs2267010 0 21864366 +22 rs5759636 0 21868698 +22 rs2071436 0 21871488 +22 rs2267013 0 21875879 +22 rs6003566 0 21889806 +22 rs2256725 0 21892891 +22 rs12160770 0 21892925 +22 rs5751611 0 21896019 +22 rs762601 0 21898858 +22 rs2156921 0 21899063 +22 rs4822375 0 21905642 diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.ped --- a/test-data/tinywga.ped Thu Oct 29 13:34:44 2009 -0400 +++ b/test-data/tinywga.ped Thu Oct 29 17:57:30 2009 -0400 @@ -1,90 +1,40 @@ -CH18526 NA18526 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18524 NA18524 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18529 NA18529 0 0 2 1 C C A A T C A G T C T C T C C C G A G C -CH18558 NA18558 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18532 NA18532 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18561 NA18561 0 0 1 1 C C A A C C G G T C C C T C C C G A G C -CH18562 NA18562 0 0 1 1 C C G A T C A G T C C C T C C C G A G C -CH18537 NA18537 0 0 2 2 C C A A T C A G C C C C C C C C A A C C -CH18603 NA18603 0 0 1 2 C C G A T C A G C C C C C C C C A A C C -CH18540 NA18540 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18605 NA18605 0 0 1 1 C C A A T T A A C C C C C C C C A A C C -CH18542 NA18542 0 0 2 1 C C G A T C G G C C C C C C C C A A C C -CH18545 NA18545 0 0 2 1 C C G A T C A G T C C C T C C C G A G C -CH18572 NA18572 0 0 1 2 C C A A T C A G C C C C C C C C A A G C -CH18547 NA18547 0 0 2 2 C C G A T C A G T C C C T C C C G A G C -CH18609 NA18609 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18550 NA18550 0 0 2 1 C C G G T T A A T C C C T C T C G A G C -CH18608 NA18608 0 0 1 1 C C G A T C G G C C C C C C C C A A C C -CH18552 NA18552 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18611 NA18611 0 0 1 1 C C G A T C A G T C C C T C C C G A G C -CH18555 NA18555 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18564 NA18564 0 0 2 2 C C A A T C G G C C C C C C C C A A C C -CH18566 NA18566 0 0 2 1 C C A A T C A G C C C C C C T C A A C C -CH18563 NA18563 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18570 NA18570 0 0 2 1 C C A A T C A G T C T C T C C C G A G C -CH18612 NA18612 0 0 1 2 C C A A T C A A T C T C T C C C G A G C -CH18571 NA18571 0 0 2 1 C C A A T C A G C C C C C C C C A A C C -CH18620 NA18620 0 0 1 1 C C A A C C G G T C T C T C C C G A G C -CH18621 NA18621 0 0 1 1 C C G G T T A A T C C C T C C C G A G C -CH18594 NA18594 0 0 2 1 C C A A T T A A C C C C C C C C A A G C -CH18622 NA18622 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -CH18573 NA18573 0 0 2 2 C C A A T C A G C C C C C C C C A A C C -CH18623 NA18623 0 0 1 1 C C G A T C G G C C C C C C C C A A C C -CH18576 NA18576 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18577 NA18577 0 0 2 1 C C A A T C A G C C C C C C C C A A G C -CH18624 NA18624 0 0 1 1 C C A A T C A G C C C C C C C C A A C C -CH18579 NA18579 0 0 2 1 C C A A T C A G T C T C T C T C G A G C -CH18632 NA18632 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -CH18582 NA18582 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18633 NA18633 0 0 1 1 C C G A T C G G C C C C C C C C A A C C -CH18635 NA18635 0 0 1 2 C C A A T C G G C C C C C C C C A A C C -CH18592 NA18592 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18636 NA18636 0 0 1 1 C C A A T C A A T C T C T C C C G A G C -CH18593 NA18593 0 0 2 2 C C A A C C G G T C T C T C C C G A G C -CH18637 NA18637 0 0 1 1 C C A A T C A G T C T C T C C C G A G C -JA18942 NA18942 0 0 2 2 C C A A C C A G C C C C C C C C A A C C -JA18940 NA18940 0 0 1 2 C C A A T C A G C C C C C C C C A A G C -JA18951 NA18951 0 0 2 2 C C G A T C A G C C C C C C C C A A C C -JA18943 NA18943 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -JA18947 NA18947 0 0 2 2 C C G A T T A A C C C C C C C C A A G C -JA18944 NA18944 0 0 1 2 C C A A T C A G T C T C T C C C G A G C -JA18945 NA18945 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -JA18949 NA18949 0 0 2 2 C C G A T C G G C C C C C C C C A A C C -JA18948 NA18948 0 0 1 2 C C G A T C G G C C C C C C C C A A C C -JA18952 NA18952 0 0 1 2 C C A A T C A G C C C C C C C C A A C C -JA18956 NA18956 0 0 2 2 C C A A C C A G T C T C T C C C G A G C -JA18964 NA18964 0 0 2 2 C C A A T T A A C C C C C C C C A A G C -JA18953 NA18953 0 0 1 1 C C A A T C A G C C C C C C T C A A C C -JA18968 NA18968 0 0 2 2 C C A A C C G G C C C C C C C C A A C C -JA18959 NA18959 0 0 1 2 C C G A T C G G C C C C C C C C A A C C -JA18969 NA18969 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -JA18960 NA18960 0 0 1 2 C C A A T C A G T C T C T C C C G A G C -JA18961 NA18961 0 0 1 2 C C A A C C A G C C C C C C C C A A C C -JA18972 NA18972 0 0 2 2 C C G A T T A A T T T C T T C C G G G G -JA18965 NA18965 0 0 1 2 C C A A T T A A C C C C C C C C A A C C -JA18973 NA18973 0 0 2 2 C C A A C C G G C C C C C C T C A A C C -JA18966 NA18966 0 0 1 2 C C G A T C A G T C C C T C C C G A G C -JA18975 NA18975 0 0 2 2 C C A A C C G G C C C C C C C C A A G C -JA18967 NA18967 0 0 1 2 C C A A C C G G C C C C C C C C A A G C -JA18976 NA18976 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -JA18978 NA18978 0 0 2 2 C C G A T C G G C C C C C C C C A A C C -JA18970 NA18970 0 0 1 1 C C G G T T A A T T C C T T C C G G G G -JA18980 NA18980 0 0 2 2 C C A A T C A G T C T C T C C C G A G C -JA18995 NA18995 0 0 1 1 C C A A T T A A C C C C C C C C A A G G -JA18981 NA18981 0 0 2 2 C C A A T C A G C C C C C C C C A A G C -JA18971 NA18971 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -JA18974 NA18974 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -JA18987 NA18987 0 0 2 2 C C A A C C G G C C C C C C C C A A C C -JA18990 NA18990 0 0 1 1 C C A A T C G G C C C C C C C C A A G C -JA18991 NA18991 0 0 2 2 C C A A C C G G C C C C C C C C A A C C -JA18994 NA18994 0 0 1 2 C C G A T C A G C C C C C C C C A A G C -JA18992 NA18992 0 0 2 2 C C A A T C A G C C C C C C T C A A C C -JA18997 NA18997 0 0 2 2 C C A A C C G G C C C C C C C C A A C C -JA18998 NA18998 0 0 2 2 C C A A C C G G C C C C C C T C A A C C -JA19000 NA19000 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -JA19005 NA19005 0 0 1 2 C C A A C C G G C C C C C C C C A A G C -JA18999 NA18999 0 0 2 2 C C A A T C A G C C C C C C C C A A C C -JA19007 NA19007 0 0 1 2 C C A A T C A G C C C C C C C C A A G C -JA19003 NA19003 0 0 2 2 C C A A T C G G C C C C C C C C A A C C -JA19012 NA19012 0 0 1 2 C C A A 0 0 G G C C C C C C 0 0 A A C C +101 1 3 2 2 2 2 2 4 2 1 3 3 3 3 3 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 1 1 2 2 2 2 3 1 3 1 2 1 0 0 2 2 1 3 3 1 1 3 +101 2 0 0 2 1 2 2 4 2 1 3 3 3 3 3 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 1 1 2 2 2 2 3 1 3 1 2 1 3 3 2 2 1 3 3 1 1 3 +101 3 0 0 1 1 2 2 4 4 1 3 3 3 3 3 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 1 3 2 4 3 3 1 1 3 3 +105 1 3 2 2 2 2 2 4 2 3 3 3 3 3 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 3 1 1 1 2 1 0 0 2 2 1 1 3 3 1 1 +105 2 0 0 2 1 2 2 4 4 3 3 3 3 3 1 2 2 1 3 1 2 3 1 2 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +105 3 0 0 1 1 4 2 2 2 3 3 3 3 3 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3 +112 1 3 2 1 2 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +112 2 0 0 2 1 2 2 2 2 3 3 1 1 1 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +112 3 0 0 1 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 2 2 1 1 2 2 4 2 4 4 1 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +117 1 3 2 2 2 2 2 4 2 3 3 3 3 3 3 4 2 1 1 2 2 1 1 2 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 2 1 1 3 3 1 1 +117 2 0 0 2 1 2 2 4 4 1 3 3 3 3 3 2 2 1 3 2 2 1 1 2 2 4 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +117 3 0 0 1 1 2 2 4 2 3 3 3 3 3 3 4 2 1 1 2 2 1 1 2 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +12 1 3 2 1 2 2 2 4 4 1 3 3 3 3 3 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 3 3 2 4 3 3 1 1 3 3 +12 2 0 0 2 1 2 2 4 4 1 3 3 3 3 3 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 3 3 2 4 3 3 1 1 3 3 +12 3 0 0 1 1 2 2 4 2 1 3 1 3 3 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 3 3 2 4 3 3 1 1 3 3 +13 1 3 2 1 2 4 2 4 2 1 3 3 3 3 1 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 3 4 1 1 2 2 4 2 1 1 3 1 1 1 3 3 2 4 3 3 1 1 3 3 +13 2 0 0 2 1 4 2 2 2 3 3 1 3 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 0 0 0 0 3 3 1 1 3 3 +13 3 0 0 1 1 2 2 4 4 1 3 3 3 3 3 2 2 1 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 3 1 2 2 2 2 1 1 3 1 1 1 3 3 2 2 3 3 1 1 3 3 +1334 1 10 11 1 2 2 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 4 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1334 10 0 0 1 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 2 2 1 1 4 2 4 2 4 4 1 1 3 4 1 1 2 2 4 2 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3 +1334 11 0 0 2 1 2 2 2 2 3 3 1 1 1 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1334 12 0 0 1 1 4 2 2 2 3 3 1 3 1 1 2 2 3 3 2 2 1 1 2 2 4 2 4 4 1 1 3 4 1 1 2 2 4 2 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3 +1334 13 0 0 2 1 4 2 4 2 3 3 1 3 3 1 4 2 1 3 2 2 1 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1334 2 12 13 2 2 4 4 2 2 3 3 1 3 1 1 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 3 3 1 1 2 2 4 4 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3 +1340 1 9 10 1 2 4 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 3 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1340 10 0 0 2 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 3 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1340 11 0 0 1 1 4 2 4 2 3 3 1 3 3 1 4 2 1 3 2 2 1 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1340 12 0 0 2 1 2 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 4 2 4 2 2 4 3 1 4 4 1 1 4 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1340 2 11 12 2 2 2 2 4 2 3 3 1 3 3 1 4 2 1 3 1 2 3 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1340 9 0 0 1 1 4 4 2 2 3 3 1 1 1 1 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 3 3 1 1 2 2 4 4 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1341 1 11 12 1 1 2 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 4 2 4 2 2 4 3 1 4 4 1 1 0 0 2 2 1 1 1 1 1 1 3 3 2 2 1 1 3 3 1 1 +1341 11 0 0 1 1 2 2 2 2 3 3 1 1 1 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 4 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1341 12 0 0 2 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 2 2 1 1 4 2 4 2 4 4 1 1 3 4 1 1 4 2 4 2 3 1 1 1 2 1 3 3 2 2 1 1 3 3 1 1 +1341 13 0 0 1 1 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1341 14 0 0 2 1 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1341 2 13 14 2 1 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1344 1 12 13 1 1 2 2 4 4 3 3 3 3 3 3 4 4 1 1 2 2 1 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 2 1 1 3 3 1 1 +1344 12 0 0 1 1 2 2 4 2 3 3 1 3 3 1 4 2 1 3 1 2 3 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1344 13 0 0 2 1 2 2 4 2 3 3 1 3 3 1 4 2 1 3 1 2 3 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1345 12 0 0 1 1 4 2 4 2 3 3 3 3 3 1 2 2 1 3 2 2 1 1 4 2 4 2 4 4 1 1 3 4 1 1 4 2 4 2 3 1 1 1 2 1 3 3 2 2 1 1 3 3 1 1 diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.pphe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tinywga.pphe Thu Oct 29 17:57:30 2009 -0400 @@ -0,0 +1,42 @@ +FID IID c1 c2 +101 1 0.545103 0.918463 +101 2 0.491123 0.309616 +101 3 0.651988 0.048298 +105 1 0.424657 0.853486 +105 2 0.813036 0.767600 +105 3 0.042279 0.786226 +112 1 0.538062 0.116152 +112 2 0.038197 0.911567 +112 3 0.991881 0.647654 +117 1 0.553303 0.672842 +117 2 0.231171 0.197314 +117 3 0.245332 0.517846 +12 1 0.311838 0.108011 +12 2 0.764390 0.968887 +12 3 0.393993 0.857926 +13 1 0.291201 0.288068 +13 2 0.113351 0.782368 +13 3 0.130878 0.927257 +1334 1 0.539897 0.932499 +1334 10 0.204083 0.893518 +1334 11 0.441118 0.900758 +1334 12 0.325336 0.271307 +1334 13 0.910762 0.636606 +1334 2 0.630607 0.537458 +1340 1 0.598157 0.813064 +1340 10 0.162311 0.956523 +1340 11 0.891147 0.987962 +1340 12 0.302027 0.786424 +1340 2 0.375225 0.338616 +1340 9 0.691503 0.965552 +1341 1 0.971333 0.115437 +1341 11 0.171352 0.873480 +1341 12 0.778930 0.179902 +1341 13 0.092468 0.050435 +1341 14 0.898538 0.913943 +1341 2 0.969939 0.086483 +1344 1 0.318008 0.376770 +1344 12 0.290673 0.870879 +1344 13 0.716322 0.087859 +1345 12 0.886441 0.717204 +

1 0

[hg] galaxy 2928: Specify color for feature tracks in one place ...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fabb2f6abc45 changeset: 2928:fabb2f6abc45 user: James Taylor <james(a)jamestaylor.org> date: Wed Oct 28 15:09:05 2009 -0400 description: Specify color for feature tracks in one place (eventually should be configurable) diffstat: static/scripts/trackster.js | 11 ++++++----- 1 files changed, 6 insertions(+), 5 deletions(-) diffs (51 lines): diff -r edb48f2816b5 -r fabb2f6abc45 static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Oct 27 22:34:30 2009 -0400 +++ b/static/scripts/trackster.js Wed Oct 28 15:09:05 2009 -0400 @@ -240,10 +240,10 @@ var min_label = $("<div class='yaxislabel'>" + track.min_value + "</div>"); var max_label = $("<div class='yaxislabel'>" + track.max_value + "</div>"); - max_label.css({ position: "relative", top: "20px" }); + max_label.css({ position: "relative", top: "35px" }); max_label.prependTo(track.container_div) - min_label.css({ position: "relative", top: track.height_px + 50 + "px", }); + min_label.css({ position: "relative", top: track.height_px + 32 + "px", }); min_label.prependTo(track.container_div); track.draw(); @@ -324,6 +324,7 @@ this.show_labels_scale = 0.001; this.showing_labels = false; this.vertical_gap = 10; + this.base_color = "#2C3143"; }; $.extend( FeatureTrack.prototype, TiledTrack.prototype, { init: function() { @@ -427,7 +428,7 @@ new_canvas.get(0).height = height; // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); var ctx = new_canvas.get(0).getContext("2d"); - ctx.fillStyle = "#000"; + ctx.fillStyle = this.base_color; ctx.font = "10px monospace"; ctx.textAlign = "right"; @@ -462,7 +463,7 @@ ctx.fillStyle = LEFT_STRAND; } ctx.fillRect(f_start, y_center, f_end - f_start, 10); - ctx.fillStyle = "#000"; + ctx.fillStyle = this.base_color; } for (var k = 0, k_len = blocks.length; k < k_len; k++) { @@ -497,7 +498,7 @@ ctx.fillStyle = LEFT_STRAND_INV; } ctx.fillRect(f_start, y_center, f_end - f_start, 10); - ctx.fillStyle = "#000"; + ctx.fillStyle = this.base_color; } } }

1 0

[hg] galaxy 2931: Fix page migration for mysql
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/86cc0b2b9e09 changeset: 2931:86cc0b2b9e09 user: James Taylor <james(a)jamestaylor.org> date: Thu Oct 29 10:06:11 2009 -0400 description: Fix page migration for mysql diffstat: lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py | 17 ++++++-- 1 files changed, 13 insertions(+), 4 deletions(-) diffs (29 lines): diff -r 1aafea08f0e8 -r 86cc0b2b9e09 lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py --- a/lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py Thu Oct 29 09:25:52 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py Thu Oct 29 10:06:11 2009 -0400 @@ -21,12 +21,21 @@ Page_table = Table( "page", metadata, autoload=True ) - i = Index( "ix_page_slug", Page_table.c.slug ) - i.drop() + try: + + # Sqlite doesn't support .alter, so we need to drop an recreate - i = Index( "ix_page_slug", Page_table.c.slug, unique=False ) - i.create() + i = Index( "ix_page_slug", Page_table.c.slug ) + i.drop() + + i = Index( "ix_page_slug", Page_table.c.slug, unique=False ) + i.create() + except: + + # Mysql doesn't have a named index, but alter should work + + Page_table.c.slug.alter( unique=False ) def downgrade(): metadata.reflect()

1 0

[hg] galaxy 2930: Fix for Nate's get_platform monkey patch.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1aafea08f0e8 changeset: 2930:1aafea08f0e8 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Oct 29 09:25:52 2009 -0400 description: Fix for Nate's get_platform monkey patch. diffstat: lib/galaxy/__init__.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r a9426ddbe468 -r 1aafea08f0e8 lib/galaxy/__init__.py --- a/lib/galaxy/__init__.py Wed Oct 28 15:09:10 2009 -0400 +++ b/lib/galaxy/__init__.py Thu Oct 29 09:25:52 2009 -0400 @@ -12,7 +12,7 @@ import os, sys from distutils.sysconfig import get_config_vars -if ( os.uname()[-1] in ( 'i386', 'ppc' ) and sys.platform == 'darwin' and sys.prefix.startswith( '/System' ) ) or \ +if ( os.uname()[-1] in ( 'i386', 'ppc' ) and sys.platform == 'darwin' and os.path.abspath( sys.prefix ).startswith( '/System' ) ) or \ ( sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip() ): # Has to be before anything imports pkg_resources def _get_platform_monkeypatch():

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[hg] galaxy 2929: Pages can now be deleted. Pages have a 'publis...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a9426ddbe468 changeset: 2929:a9426ddbe468 user: James Taylor <james(a)jamestaylor.org> date: Wed Oct 28 15:09:10 2009 -0400 description: Pages can now be deleted. Pages have a 'published' attribute that determines whether they are publicly accessible. There is now a list of all published pages from all users diffstat: lib/galaxy/model/mapping.py | 2 + lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py | 35 ++ lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py | 34 ++ lib/galaxy/web/controllers/page.py | 141 +++++++- lib/galaxy/web/framework/helpers/grids.py | 2 +- templates/base_panels.mako | 3 + 6 files changed, 194 insertions(+), 23 deletions(-) diffs (332 lines): diff -r fabb2f6abc45 -r a9426ddbe468 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Wed Oct 28 15:09:05 2009 -0400 +++ b/lib/galaxy/model/mapping.py Wed Oct 28 15:09:10 2009 -0400 @@ -545,6 +545,8 @@ ForeignKey( "page_revision.id", use_alter=True, name='page_latest_revision_id_fk' ), index=True ), Column( "title", TEXT ), Column( "slug", TEXT, unique=True, index=True ), + Column( "published", Boolean, index=True, default=False ), + Column( "deleted", Boolean, index=True, default=False ), ) PageRevision.table = Table( "page_revision", metadata, diff -r fabb2f6abc45 -r a9426ddbe468 lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py Wed Oct 28 15:09:10 2009 -0400 @@ -0,0 +1,35 @@ +""" +Migration script to add columns for tracking whether pages are deleted and +publicly accessible. +""" + +from sqlalchemy import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) + +def upgrade(): + + print __doc__ + metadata.reflect() + + Page_table = Table( "page", metadata, autoload=True ) + + c = Column( "published", Boolean, index=True, default=False ) + c.create( Page_table ) + assert c is Page_table.c.published + + c = Column( "deleted", Boolean, index=True, default=False ) + c.create( Page_table ) + assert c is Page_table.c.deleted + +def downgrade(): + metadata.reflect() + + Page_table = Table( "page", metadata, autoload=True ) + Page_table.c.published.drop() + Page_table.c.deleted.drop() diff -r fabb2f6abc45 -r a9426ddbe468 lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py Wed Oct 28 15:09:10 2009 -0400 @@ -0,0 +1,34 @@ +""" +Remove unique constraint from page slugs to allow creating a page with +the same slug as a deleted page. +""" + +from sqlalchemy import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) + +def upgrade(): + print __doc__ + metadata.reflect() + + Page_table = Table( "page", metadata, autoload=True ) + + i = Index( "ix_page_slug", Page_table.c.slug ) + i.drop() + + i = Index( "ix_page_slug", Page_table.c.slug, unique=False ) + i.create() + + +def downgrade(): + metadata.reflect() + #Page_table = Table( "page", metadata, autoload=True ) + #Page_table.c.slug.alter( unique=True ) diff -r fabb2f6abc45 -r a9426ddbe468 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Wed Oct 28 15:09:05 2009 -0400 +++ b/lib/galaxy/web/controllers/page.py Wed Oct 28 15:09:10 2009 -0400 @@ -6,16 +6,27 @@ VALID_SLUG_RE = re.compile( "^[a-z0-9\-]+$" ) +def format_bool( b ): + if b: + return "yes" + else: + return "" + +class PublicURLColumn( grids.GridColumn ): + def get_value( self, trans, grid, item ): + username = trans.user.username or "???" + return username + "/" + item.slug + def get_link( self, trans, grid, item ): + if trans.user.username: + return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) + else: + return None + +class OwnerColumn( grids.GridColumn ): + def get_value( self, trans, grid, item ): + return item.user.username + class PageListGrid( grids.Grid ): - class URLColumn( grids.GridColumn ): - def get_value( self, trans, grid, item ): - username = trans.user.username or "???" - return username + "/" + item.slug - def get_link( self, trans, grid, item ): - if trans.user.username: - return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) - else: - return None # Grid definition use_panels = True title = "Your pages" @@ -23,7 +34,8 @@ default_sort_key = "-create_time" columns = [ grids.GridColumn( "Title", key="title", attach_popup=True ), - URLColumn( "Public URL" ), + PublicURLColumn( "Public URL" ), + grids.GridColumn( "Published", key="published", format=format_bool ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -32,25 +44,67 @@ ] operations = [ grids.GridOperation( "View", allow_multiple=False, url_args=dict( action='display') ), - grids.GridOperation( "Edit", allow_multiple=False, url_args=dict( action='edit') ) + grids.GridOperation( "Edit name/id", allow_multiple=False, url_args=dict( action='edit') ), + grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ), + grids.GridOperation( "Delete" ), + grids.GridOperation( "Publish", condition=( lambda item: not item.published ) ), + grids.GridOperation( "Unpublish", condition=( lambda item: item.published ) ), ] def apply_default_filter( self, trans, query, **kwargs ): - return query.filter_by( user=trans.user ) + return query.filter_by( user=trans.user, deleted=False ) + +class PageAllPublishedGrid( grids.Grid ): + # Grid definition + use_panels = True + title = "Published pages from all users" + model_class = model.Page + default_sort_key = "-create_time" + columns = [ + grids.GridColumn( "Title", key="title" ), + PublicURLColumn( "Public URL" ), + OwnerColumn( "Published by" ), + grids.GridColumn( "Created", key="create_time", format=time_ago ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), + ] + def apply_default_filter( self, trans, query, **kwargs ): + return query.filter_by( deleted=False, published=True ) class PageController( BaseController ): - list = PageListGrid() + _page_list = PageListGrid() + _all_published_list = PageAllPublishedGrid() @web.expose - @web.require_admin + @web.require_login() def index( self, trans, *args, **kwargs ): + # Handle operation + if 'operation' in kwargs and 'id' in kwargs: + session = trans.sa_session + operation = kwargs['operation'] + ids = util.listify( kwargs['id'] ) + for id in ids: + item = session.query( model.Page ).get( trans.security.decode_id( id ) ) + if operation == "Delete": + item.deleted = True + elif operation == "Publish": + item.published = True + elif operation == "Unpublish": + item.published = False + session.flush() # Build grid - grid = self.list( trans, *args, **kwargs ) + grid = self._page_list( trans, *args, **kwargs ) # Render grid wrapped in panels return trans.fill_template( "page/index.mako", grid=grid ) @web.expose - @web.require_admin + @web.require_login() + def list_published( self, trans, *args, **kwargs ): + grid = self._all_published_list( trans, *args, **kwargs ) + # Render grid wrapped in panels + return trans.fill_template( "page/index.mako", grid=grid ) + + + @web.expose @web.require_login( "create pages" ) def create( self, trans, page_title="", page_slug="" ): """ @@ -65,7 +119,7 @@ page_slug_err = "Page id is required" elif not VALID_SLUG_RE.match( page_slug ): page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character" - elif trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug ).first(): + elif trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first(): page_slug_err = "Page id must be unique" else: # Create the new stored workflow @@ -98,9 +152,50 @@ template="page/create.mako" ) @web.expose - @web.require_admin + @web.require_login( "create pages" ) + def edit( self, trans, id, page_title="", page_slug="" ): + """ + Create a new page + """ + encoded_id = id + id = trans.security.decode_id( id ) + session = trans.sa_session + page = session.query( model.Page ).get( id ) + user = trans.user + assert page.user == user + page_title_err = page_slug_err = "" + if trans.request.method == "POST": + if not page_title: + page_title_err = "Page name is required" + elif not page_slug: + page_slug_err = "Page id is required" + elif not VALID_SLUG_RE.match( page_slug ): + page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character" + elif page_slug == page.slug or trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first(): + page_slug_err = "Page id must be unique" + else: + page.title = page_title + page.slug = page_slug + session.flush() + # Display the management page + return trans.response.send_redirect( web.url_for( action='index' ) ) + else: + page_title = page.title + page_slug = page.slug + return trans.show_form( + web.FormBuilder( web.url_for( id=encoded_id ), "Edit page attributes", submit_text="Submit" ) + .add_text( "page_title", "Page title", value=page_title, error=page_title_err ) + .add_text( "page_slug", "Page identifier", value=page_slug, error=page_slug_err, + help="""A unique identifier that will be used for + public links to this page. A default is generated + from the page title, but can be edited. This field + must contain only lowercase letters, numbers, and + the '-' character.""" ), + template="page/create.mako" ) + + @web.expose @web.require_login( "edit pages" ) - def edit( self, trans, id ): + def edit_content( self, trans, id ): """ Render the main page editor interface. """ @@ -110,7 +205,7 @@ return trans.fill_template( "page/editor.mako", page=page ) @web.expose - @web.require_admin + @web.require_login() def save( self, trans, id, content ): id = trans.security.decode_id( id ) page = trans.sa_session.query( model.Page ).get( id ) @@ -126,10 +221,12 @@ trans.sa_session.flush() @web.expose - @web.require_admin + @web.require_login() def display( self, trans, id ): id = trans.security.decode_id( id ) page = trans.sa_session.query( model.Page ).get( id ) + if page.user is not trans.user: + error( "Page is not owned by current user" ) return trans.fill_template( "page/display.mako", page=page ) @web.expose @@ -138,7 +235,7 @@ user = session.query( model.User ).filter_by( username=username ).first() if user is None: raise web.httpexceptions.HTTPNotFound() - page = trans.sa_session.query( model.Page ).filter_by( user=user, slug=slug ).first() + page = trans.sa_session.query( model.Page ).filter_by( user=user, slug=slug, deleted=False, published=True ).first() if page is None: raise web.httpexceptions.HTTPNotFound() return trans.fill_template( "page/display.mako", page=page ) diff -r fabb2f6abc45 -r a9426ddbe468 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Wed Oct 28 15:09:05 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Wed Oct 28 15:09:10 2009 -0400 @@ -279,7 +279,7 @@ temp['id'] = item.id return temp else: - return dict( operation=operation.label, id=item.id ) + return dict( operation=self.label, id=item.id ) def allowed( self, item ): if self.condition: diff -r fabb2f6abc45 -r a9426ddbe468 templates/base_panels.mako --- a/templates/base_panels.mako Wed Oct 28 15:09:05 2009 -0400 +++ b/templates/base_panels.mako Wed Oct 28 15:09:10 2009 -0400 @@ -243,6 +243,9 @@ <li><hr style="color: inherit; background-color: gray"/></li> <li><a target="galaxy_main" href="${h.url_for( controller='history', action='list' )}">Histories</a></li> <li><a target="galaxy_main" href="${h.url_for( controller='dataset', action='list' )}">Datasets</a></li> + %if app.config.get_bool( 'enable_pages', False ): + <li><a href="${h.url_for( controller='page' )}">Pages</a></li> + %endif %endif </ul> </div>

1 0

[hg] galaxy 2927: trackster: y-axis labels for linetracks, thin/...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/edb48f2816b5 changeset: 2927:edb48f2816b5 user: Kanwei Li <kanwei(a)gmail.com> date: Tue Oct 27 22:34:30 2009 -0400 description: trackster: y-axis labels for linetracks, thin/thick blocks are correct for featuretracks, messages when data is loading and being indexed diffstat: lib/galaxy/visualization/tracks/data/interval_index.py | 4 +- static/scripts/trackster.js | 171 ++++++++++++--------- static/trackster.css | 10 + templates/tracks/browser.mako | 4 - 4 files changed, 110 insertions(+), 79 deletions(-) diffs (326 lines): diff -r ea0342f2df03 -r edb48f2816b5 lib/galaxy/visualization/tracks/data/interval_index.py --- a/lib/galaxy/visualization/tracks/data/interval_index.py Tue Oct 27 15:11:41 2009 -0400 +++ b/lib/galaxy/visualization/tracks/data/interval_index.py Tue Oct 27 22:34:30 2009 -0400 @@ -35,8 +35,8 @@ pass try: - payload['exon_start'] = int(feature[6]) - payload['exon_end'] = int(feature[7]) + payload['thick_start'] = int(feature[6]) + payload['thick_end'] = int(feature[7]) except IndexError: pass diff -r ea0342f2df03 -r edb48f2816b5 static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Oct 27 15:11:41 2009 -0400 +++ b/static/scripts/trackster.js Tue Oct 27 22:34:30 2009 -0400 @@ -5,6 +5,8 @@ var DENSITY = 1000, DATA_ERROR = "There was an error in indexing this dataset.", DATA_NONE = "No data for this chrom/contig.", + DATA_PENDING = "Currently indexing... please wait", + DATA_LOADING = "Loading data...", CACHED_TILES = 50, CACHED_DATA = 20, CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"), @@ -34,11 +36,11 @@ function commatize( number ) { number += ''; // Convert to string - var rgx = /(\d+)(\d{3})/; - while (rgx.test(number)) { - number = number.replace(rgx, '$1' + ',' + '$2'); - } - return number; + var rgx = /(\d+)(\d{3})/; + while (rgx.test(number)) { + number = number.replace(rgx, '$1' + ',' + '$2'); + } + return number; } var View = function( chrom, max_high ) { this.chrom = chrom; @@ -88,7 +90,7 @@ $("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>'); }, zoom_in: function ( point ) { - if (this.max_high === 0 || this.high - this.low < 5) { + if (this.max_high === 0 || this.high - this.low < 30) { return; } @@ -96,6 +98,7 @@ this.center = point / $(document).width() * (this.high - this.low) + this.low; } this.zoom_level += 1; + this.redraw(); }, zoom_out: function () { if (this.max_high === 0) { @@ -106,6 +109,7 @@ return; } this.zoom_level -= 1; + this.redraw(); } }); @@ -137,13 +141,13 @@ resolution = Math.max( resolution, 1 ); resolution = Math.min( resolution, 100000 ); - var parent_element = $("<div style='position: relative;'></div>"); + var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); this.content_div.append( parent_element ); var w = this.content_div.width(), h = this.content_div.height(), - w_scale = w / range; + w_scale = w / range; var tile_element; // Index of first tile that overlaps visible region @@ -211,21 +215,38 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, { init: function() { var track = this; + track.content_div.text(DATA_LOADING); $.getJSON( data_url, { stats: true, track_type: track.track_type, chrom: track.view.chrom, low: null, high: null, dataset_id: track.dataset_id }, function ( data ) { if (!data || data == "error") { track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); + track.content_div.text(DATA_ERROR); } else if (data == "no data") { track.container_div.addClass("nodata"); - track.content_div.text(DATA_NONE); + track.content_div.text(DATA_NONE); + } else if (data == "pending") { + track.container_div.addClass("pending"); + track.content_div.text(DATA_PENDING); + setTimeout(function() { track.init(); }, 5000); } else { + track.content_div.text(""); track.content_div.css( "height", track.height_px + "px" ); track.min_value = data.min; track.max_value = data.max; track.vertical_range = track.max_value - track.min_value; - track.view.redraw(); + + // Draw y-axis labels + var min_label = $("<div class='yaxislabel'>" + track.min_value + "</div>"); + var max_label = $("<div class='yaxislabel'>" + track.max_value + "</div>"); + + max_label.css({ position: "relative", top: "20px" }); + max_label.prependTo(track.container_div) + + min_label.css({ position: "relative", top: track.height_px + 50 + "px", }); + min_label.prependTo(track.container_div); + + track.draw(); } }); }, @@ -307,16 +328,22 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, { init: function() { var track = this; + track.content_div.text(DATA_LOADING); $.getJSON( data_url, { track_type: track.track_type, low: track.view.max_low, high: track.view.max_high, dataset_id: track.dataset_id, chrom: track.view.chrom }, function ( data ) { if (data == "error") { track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); + track.content_div.text(DATA_ERROR); } else if (data.length === 0 || data == "no data") { track.container_div.addClass("nodata"); - track.content_div.text(DATA_NONE); + track.content_div.text(DATA_NONE); + } else if (data == "pending") { + track.container_div.addClass("pending"); + track.content_div.text(DATA_PENDING); + setTimeout(function() { track.init(); }, 5000); } else { + track.content_div.text(""); track.content_div.css( "height", track.height_px + "px" ); track.values = data; track.calc_slots(); @@ -412,68 +439,66 @@ f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), y_center = this.slots[feature.name] * this.vertical_gap; - if (feature.strand && this.showing_labels) { - if (feature.strand == "+") { - ctx.fillStyle = RIGHT_STRAND; - } else if (feature.strand == "-") { - ctx.fillStyle = LEFT_STRAND; + var thickness, y_start, thick_start = null, thick_end = null; + if (feature.thick_start && feature.thick_end) { + thick_start = Math.floor( Math.max(0, (feature.thick_start - tile_low) * w_scale) ); + thick_end = Math.ceil( Math.min(width, (feature.thick_end - tile_low) * w_scale) ); + } + if (!this.showing_labels) { + // Non-detail levels + ctx.fillRect(f_start, y_center + 5, f_end - f_start, 1); + } else { + // Showing labels, blocks, details + if (ctx.fillText) { + ctx.fillText(feature.name, f_start - 1, y_center + 8); } - ctx.fillRect(f_start, y_center, f_end - f_start, 10); - ctx.fillStyle = "#000"; - } else { - ctx.fillStyle = "#000"; - ctx.fillRect(f_start, y_center + 5, f_end - f_start, 1); - } - - if (this.showing_labels && ctx.fillText) { - ctx.fillText(feature.name, f_start - 1, y_center + 8); - } - - // If there is no thickStart/thickEnd, draw the whole thing - // as thick. - var exon_start, exon_end; - if (feature.exon_start && feature.exon_end) { - exon_start = Math.floor( Math.max(0, (feature.exon_start - tile_low) * w_scale) ); - exon_end = Math.ceil( Math.min(width, (feature.exon_end - tile_low) * w_scale) ); - } else { - exon_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ); - exon_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ); - } - - if (this.showing_labels) { - // If there are no blocks, we treat the feature as one - // big exon - var blocks = feature.blocks; - var arrows_in_blocks = false; - if ( ! blocks ) { - blocks = [[feature.start,feature.end]]; - arrows_in_blocks = true - } - for (var k = 0, k_len = blocks.length; k < k_len; k++) { - var block = blocks[k], - block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), - block_end = Math.ceil( Math.min(width, (block[1] - tile_low) * w_scale) ); - var thickness, y_start; - if (exon_start && block_start >= exon_start && block_end <= exon_end) { - thickness = 9; - y_start = 1; - ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); - if ( feature.strand && arrows_in_blocks ) { - if (feature.strand == "+") { - ctx.fillStyle = RIGHT_STRAND_INV; - } else if (feature.strand == "-") { - ctx.fillStyle = LEFT_STRAND_INV; - } - ctx.fillRect(block_start, y_center, block_end - block_start, 10); - ctx.fillStyle = "#000"; - } - } else { - thickness = 5; - y_start = 3; - ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); - } + var blocks = feature.blocks; + if (blocks) { + // Draw introns + if (feature.strand) { + if (feature.strand == "+") { + ctx.fillStyle = RIGHT_STRAND; + } else if (feature.strand == "-") { + ctx.fillStyle = LEFT_STRAND; + } + ctx.fillRect(f_start, y_center, f_end - f_start, 10); + ctx.fillStyle = "#000"; + } - // console.log(block_start, block_end); + for (var k = 0, k_len = blocks.length; k < k_len; k++) { + var block = blocks[k], + block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), + block_end = Math.ceil( Math.min(width, (block[1] - tile_low) * w_scale) ); + + // Draw the block + thickness = 5; + y_start = 3; + ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); + + if (thick_start && (block_start < thick_end || block_end > thick_start) ) { + thickness = 9; + y_start = 1; + var block_thick_start = Math.max(block_start, thick_start), + block_thick_end = Math.min(block_end, thick_end); + + ctx.fillRect(block_thick_start, y_center + y_start, block_thick_end - block_thick_start, thickness); + + } + } + } else { + // If there are no blocks, we treat the feature as one big exon + thickness = 9; + y_start = 1; + ctx.fillRect(f_start, y_center + y_start, f_end - f_start, thickness); + if ( feature.strand ) { + if (feature.strand == "+") { + ctx.fillStyle = RIGHT_STRAND_INV; + } else if (feature.strand == "-") { + ctx.fillStyle = LEFT_STRAND_INV; + } + ctx.fillRect(f_start, y_center, f_end - f_start, 10); + ctx.fillStyle = "#000"; + } } } j++; diff -r ea0342f2df03 -r edb48f2816b5 static/trackster.css --- a/static/trackster.css Tue Oct 27 15:11:41 2009 -0400 +++ b/static/trackster.css Tue Oct 27 22:34:30 2009 -0400 @@ -95,6 +95,16 @@ width: 100%; height: 100px; } + +.yaxislabel { + color: #777; +} +/* Line track needs borders to show range */ +.line-track .track-content { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; +} + .track { /* border-top: solid gray 1px; */ /* border-bottom: solid gray 1px; */ diff -r ea0342f2df03 -r edb48f2816b5 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Tue Oct 27 15:11:41 2009 -0400 +++ b/templates/tracks/browser.mako Tue Oct 27 22:34:30 2009 -0400 @@ -30,16 +30,13 @@ $(document).bind("mousewheel", function( e, delta ) { if (delta > 0) { view.zoom_in(e.pageX); - view.redraw(); } else { view.zoom_out(); - view.redraw(); } }); $(document).bind("dblclick", function( e ) { view.zoom_in(e.pageX); - view.redraw(); }); // To let the overview box be draggable @@ -96,7 +93,6 @@ }); }); })(); - view.redraw(); $(window).trigger("resize"); });

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Running Galaxy on another server
by Raghav Bhatnagar 06 Nov '09

06 Nov '09

Hi I installed a copy of Galaxy on my server under public_html Folder. I also modified the universe_wsgi.ini file and changed the host setting to 0.0.0.0. Invoking sh run.sh command, Galaxy tends to start starting : serving on 0.0.0.0:8080 view at http://127.0.0.1:8080 But http://127.0.0.1:8080 gives a "*page load error*" on viewing in browser. If I change host setting to the IP address of my server, it displays a bunch of errors and does not start Galaxy. Those errors are: - *Starting server in PID 29836. Traceback (most recent call last): File "./scripts/paster.py", line 32, in ? command.run() File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/PasteScript-1.3.6-py2.4.egg/paste/script/command.py", line 78, in run invoke(command, command_name, options, args[1:]) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/PasteScript-1.3.6-py2.4.egg/paste/script/command.py", line 117, in invoke exit_code = runner.run(args) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/PasteScript-1.3.6-py2.4.egg/paste/script/command.py", line 212, in run result = self.command() File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/PasteScript-1.3.6-py2.4.egg/paste/script/serve.py", line 232, in command server(app) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/PasteDeploy-1.3.1-py2.4.egg/paste/deploy/loadwsgi.py", line 139, in server_wrapper wsgi_app, context.global_conf, File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/PasteDeploy-1.3.1-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 1307, in server_runner serve(wsgi_app, **kwargs) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 1257, in serve threadpool_options=threadpool_options) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 1107, in __init__ RequestHandlerClass, ssl_context) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 1087, in __init__ RequestHandlerClass, ssl_context) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 328, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib/python2.4/SocketServer.py", line 330, in __init__ self.server_bind() File "/usr/lib/python2.4/BaseHTTPServer.py", line 99, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib/python2.4/SocketServer.py", line 341, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.gaierror: (-2, 'Name or service not known') galaxy.jobs INFO 2009-11-05 21:30:08,204 sending stop signal to worker thread galaxy.jobs INFO 2009-11-05 21:30:08,204 job queue stopped galaxy.jobs.runners.local INFO 2009-11-05 21:30:08,204 sending stop signal to worker threads galaxy.jobs.runners.local INFO 2009-11-05 21:30:08,205 local job runner stopped galaxy.jobs INFO 2009-11-05 21:30:08,205 sending stop signal to worker thread galaxy.jobs INFO 2009-11-05 21:30:08,206 job stopper stopped * What changes do I have to make in order to run the Galaxy on my server? -- Raghav Bhatnagar Graduate Student (CS) Viterbi School of Engineering University of Southern California

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Output Multiple Files in Galaxy
by Luqman Hakim B Abdul Hadi 05 Nov '09

05 Nov '09

Hi Galaxy team. Im pretty new to Galaxy and currently trying to put it into production. I was wondering if it is possible to have a program that outputs many output many results file and incorporate it into Galaxy? Can you give an example of how the XML looks like? Thanks loads! Luqman

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Problems with URLs of Example pics
by Andreas Kuntzagk 05 Nov '09

05 Nov '09

Hi, we have a local galaxy installation behind a apache proxy. So far it's working flawless. But now we noticed that the images referenced in the example text of Operate on Genomic Intervals don't show. If I use the "real" address of the galaxy without proxy, it's working (no config change or restart!) The generated HTML contains: <img alt="../static/operation_icons/gops_complement.gif" src="../static/operation_icons/gops_complement.gif"> This are the settings in universe_wsgi.ini [filter:proxy-prefix] use=egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix regards, Andreas

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